Standard fit report for fits of SISCA to WCVI_Herring data.
Data Scenario: WCVI_agg
Model Hypothesis: baseAggModel
Species:
Stocks:
Max Gradient: 0.0212524
Objective Function value: 4.5404989^{4}
Time to fit model: 1
PD Hessian: FALSE
No. of Non-finite SEs: 0
Figure 1: Time series of spawning biomass with scaled spawn indices (top), recruitments (second row), natural mortality (third row), and harvest rates (bottom row) for substocks of WCVI_Herring. Stocks are, from left to right,WCVI.
Figure 2: Model fits to spawn indices.
Figure 3: Probability of detection of a spawning event, with respect to spawning stock biomass. Lines show the modeled probability and the points indicate whether a spawn was detected, with 0 for no spawn detected, and 1 for a positive index.
Figure 4: Average model fits to age data. Stocks are left to right, and gears are top to bottom.
Figure 5: Model fits to age data, averaged over stock and time. Gears are top to bottom.
| \(\tau^{age}_{Red}\) | \(\tau^{age}_{SR}\) | \(\tau^{age}_{Gn}\) | \(\tau^{surv}_{Su}\) | \(\tau^{surv}_{D}\) | |
|---|---|---|---|---|---|
| WCVI | 0.754 | 0.485 | 0.669 | 0.5 | 0.5 |
Figure 6: Age-1 recruitments for all stocks. Equilibrium unfished recruitment \(R_0\) is indicated by the horizontal dashed line. Second row shows recruitment residuals on the log scale, with the average of estimated residuals shown by the horizontal red dashed line.
Figure 7: Stock-recruit curves (solid lines) and modeled recruitments (coloured points)
Figure 8: Mt
Figure 9: densityDependent M
Figure 10: Total natural mortality at age
Figure 11: Total mortality at age
Figure 12: Catch in biomass units for each stock (rows). Stacked bars show the total yearly catch for each commercial fleet, and the dead ponded fish shown with a red border.
Figure 13: Catch in biomass units for each stock (rows). Stacked bars show the total yearly catch for each commercial fleet, and the dead ponded fish shown with a red border.
Figure 14: Catch in biomass units for each stock (rows). Stacked bars show the total yearly catch for each commercial fleet, and the dead ponded fish shown with a red border.
Figure 15: Selectivity-at-age for each fleet (rows). Aggregate stock average selectivity curves are shown as thick grey lines, while sub-stock specific estimates are shown as dashed thin coloured lines.
Figure 16: Equilibrium yield curves as a function of fishing mortality rates, assuming all fishing mortality comes from the gillnet fleet.
Figure 17: Model fits to yearly WCVI stock age compositions for the reduction fleet. Grey bars are age composition observations, and lines/points are the model expected values.
Figure 18: Model fits to yearly WCVI stock age compositions for the seineRoe fleet. Grey bars are age composition observations, and lines/points are the model expected values.
Figure 19: Model fits to yearly WCVI stock age compositions for the gillnet fleet. Grey bars are age composition observations, and lines/points are the model expected values.
Figure 20: Age composition residuals for the WCVI sub-stock. Positive residuals are black black, while negative residuals are red.
Figure 21: Model fits to tail compressed yearly WCVI stock age compositions for the reduction fleet. Grey bars are age composition observations, and lines/points are the model expected values.
Figure 22: Model fits to tail compressed yearly WCVI stock age compositions for the seineRoe fleet. Grey bars are age composition observations, and lines/points are the model expected values.
Figure 23: Model fits to tail compressed yearly WCVI stock age compositions for the gillnet fleet. Grey bars are age composition observations, and lines/points are the model expected values.
| objFun | obsSurface | obsDive | ageRed | ageSR | ageGill | |
|---|---|---|---|---|---|---|
| Total | 45404.99 | 0 | 0 | 27.69 | 4.46 | -14.8 |
| WCVI | 45404.99 | 0 | 0 | 27.69 | 4.46 | -14.8 |
| V1 | |
|---|---|
| objFun | 45404.990000 |
| recDevs | 67.330000 |
| initDevs | 10.590000 |
| h | 17.430000 |
| M | -2.080000 |
| tvMdev | 0.000000 |
| IGtau_surf | 2.060000 |
| IGtau_dive | 3.170000 |
| tvSelAlpha | 0.000000 |
| tvSelBeta | 0.000000 |
| selAlphaRed | -1.380000 |
| selAlphaSR | -1.380000 |
| selAlphaGn | -1.380000 |
| selBetaRed | -1.380000 |
| selBetaSR | -1.380000 |
| selBetaGn | -1.380000 |
| lnB0 | 4.628946 |
| lnRinit | 6.476646 |
| psiSOK | -6.750000 |
| V1 | |
|---|---|
| objFun | 45404.99 |
| MDev | 0.00 |
| hDev | 0.92 |
| selAlphaDevR | 0.00 |
| selAlphaDevSR | 0.00 |
| selAlphaDevGn | 0.00 |
| selBetaDevR | 0.00 |
| selBetaDevSR | 0.00 |
| selBetaDevGn | 0.00 |
| phase | objFun | maxGrad | nPar | convCode | convMsg | time | pdHess |
|---|---|---|---|---|---|---|---|
| 1 | 46002.65 | 0.0955823 | 4 | 0 | relative convergence (4) | 0.0958667 | FALSE |
| 2 | 45993.06 | 0.0128742 | 14 | 0 | relative convergence (4) | 0.0764167 | FALSE |
| 3 | 45993.06 | 0.0054366 | 14 | 0 | relative convergence (4) | 0.0666000 | FALSE |
| 4 | 45965.21 | 0.0170467 | 17 | 0 | relative convergence (4) | 0.0789833 | FALSE |
| 5 | 45642.21 | 0.0201821 | 86 | 0 | relative convergence (4) | 0.0958500 | FALSE |
| 6 | 45467.25 | 0.0290619 | 151 | 0 | relative convergence (4) | 0.1857333 | FALSE |
| 7 | 45467.25 | 0.0112788 | 151 | 0 | relative convergence (4) | 0.0808833 | FALSE |
| 8 | 45405.14 | 0.1349876 | 152 | 0 | relative convergence (4) | 0.1660500 | FALSE |
| 9 | 45404.99 | 0.0212524 | 153 | 0 | relative convergence (4) | 0.1504167 | FALSE |
| RE | NA | NA | NA | NA | NA | NA | NA |
| est | se | gr | cv | |
|---|---|---|---|---|
| lnB0_p | 4.6289 | 0.1737 | 0.00064 | 0.0375 |
| lnRinit_p | 6.4766 | 0.1638 | 0.0031 | 0.0253 |
| lnRbar_p | 7.2315 | 0.0981 | -0.035 | 0.0136 |
| logit_ySteepness | 0.6001 | 0.3780 | 0.0012 | 0.6298 |
| lnM | -0.6933 | 0.0323 | 0.075 | 0.0466 |
| fDevs_ap | 0.8212 | 0.2628 | -2e-05 | 0.3201 |
| fDevs_ap.1 | 0.6901 | 0.2802 | 0.00061 | 0.4061 |
| fDevs_ap.2 | 0.3655 | 0.3956 | 0.00073 | 1.0824 |
| fDevs_ap.3 | 0.8556 | 0.4144 | 0.00098 | 0.4843 |
| fDevs_ap.4 | -0.6305 | 0.6955 | 0.00017 | 1.1032 |
| fDevs_ap.5 | -0.4557 | 0.7465 | 0.00012 | 1.638 |
| fDevs_ap.6 | -0.3092 | 0.8366 | 7.4e-05 | 2.7061 |
| fDevs_ap.7 | -0.1999 | 0.8878 | 5.4e-05 | 4.4409 |
| fDevs_ap.8 | -0.1210 | 0.9360 | 2.2e-05 | 7.7357 |
| fDevs_ap.9 | -0.1561 | 0.9219 | 1.7e-05 | 5.905 |
| recDevs_pt | 0.0609 | 0.0827 | -0.0016 | 1.3582 |
| recDevs_pt.1 | 0.0572 | 0.0922 | -0.00012 | 1.6112 |
| recDevs_pt.2 | 0.0458 | 0.0955 | -0.0016 | 2.0877 |
| recDevs_pt.3 | 0.1076 | 0.0997 | -0.005 | 0.9258 |
| recDevs_pt.4 | 0.2873 | 0.0862 | -0.0039 | 0.2999 |
| recDevs_pt.5 | 0.3288 | 0.0793 | -0.0075 | 0.2412 |
| recDevs_pt.6 | 0.1742 | 0.1063 | -0.0025 | 0.6101 |
| recDevs_pt.7 | 0.0673 | 0.1077 | -0.00044 | 1.5992 |
| recDevs_pt.8 | 0.1482 | 0.1049 | -0.00088 | 0.7076 |
| recDevs_pt.9 | 0.0385 | 0.1200 | 0.0011 | 3.1142 |
| recDevs_pt.10 | 0.0719 | 0.1139 | 0.0012 | 1.5831 |
| recDevs_pt.11 | -0.0990 | 0.1194 | 0.0013 | 1.2058 |
| recDevs_pt.12 | -0.1602 | 0.1089 | 0.0022 | 0.68 |
| recDevs_pt.13 | -0.0310 | 0.0955 | 0.004 | 3.0761 |
| recDevs_pt.14 | -0.2190 | 0.1276 | 9.4e-06 | 0.5824 |
| recDevs_pt.15 | -0.1928 | 0.1282 | 0.00024 | 0.6652 |
| recDevs_pt.16 | -0.0134 | 0.1060 | 0.00098 | 7.9283 |
| recDevs_pt.17 | 0.2353 | 0.0955 | 0.0027 | 0.4059 |
| recDevs_pt.18 | 0.2410 | 0.0882 | 0.0031 | 0.3662 |
| recDevs_pt.19 | 0.2224 | 0.0846 | -0.00077 | 0.3803 |
| recDevs_pt.20 | 0.3176 | 0.0837 | -0.0023 | 0.2636 |
| recDevs_pt.21 | 0.4797 | 0.0831 | -0.0049 | 0.1732 |
| recDevs_pt.22 | 0.2160 | 0.0888 | -0.0035 | 0.4113 |
| recDevs_pt.23 | 0.0969 | 0.0918 | -0.0038 | 0.9478 |
| recDevs_pt.24 | 0.3902 | 0.0907 | 0.0042 | 0.2325 |
| recDevs_pt.25 | -0.0300 | 0.0980 | 0.00046 | 3.2686 |
| recDevs_pt.26 | 0.3669 | 0.0952 | 0.0025 | 0.2595 |
| recDevs_pt.27 | 0.2070 | 0.0977 | -0.0078 | 0.4718 |
| recDevs_pt.28 | 0.1020 | 0.1009 | -0.0016 | 0.9891 |
| recDevs_pt.29 | -0.0360 | 0.0988 | 0.0036 | 2.7444 |
| recDevs_pt.30 | 0.0909 | 0.0976 | 0.0023 | 1.0737 |
| recDevs_pt.31 | 0.3155 | 0.0959 | 0.0027 | 0.3039 |
| recDevs_pt.32 | 0.3276 | 0.0920 | 0.0028 | 0.2808 |
| recDevs_pt.33 | -0.0369 | 0.0851 | -0.0013 | 2.3083 |
| recDevs_pt.34 | 0.4896 | 0.0859 | 0.0037 | 0.1754 |
| recDevs_pt.35 | -0.1229 | 0.0891 | -0.0075 | 0.7249 |
| recDevs_pt.36 | -0.0180 | 0.0845 | -0.0016 | 4.7038 |
| recDevs_pt.37 | -0.0828 | 0.0862 | -0.00076 | 1.0416 |
| recDevs_pt.38 | 0.1730 | 0.0809 | 0.00023 | 0.4679 |
| recDevs_pt.39 | 0.0720 | 0.0850 | -0.0072 | 1.1805 |
| recDevs_pt.40 | -0.0204 | 0.0854 | -0.0041 | 4.1946 |
| recDevs_pt.41 | -0.2570 | 0.0862 | 0.00074 | 0.3354 |
| recDevs_pt.42 | -0.1398 | 0.0843 | -0.0085 | 0.603 |
| recDevs_pt.43 | 0.2872 | 0.0794 | -0.013 | 0.2764 |
| recDevs_pt.44 | -0.0437 | 0.0848 | -0.01 | 1.9412 |
| recDevs_pt.45 | -0.2874 | 0.0909 | -0.0066 | 0.3164 |
| recDevs_pt.46 | -0.1330 | 0.0879 | -0.0021 | 0.6608 |
| recDevs_pt.47 | -0.0849 | 0.0855 | -0.0013 | 1.0073 |
| recDevs_pt.48 | 0.0404 | 0.0783 | -0.004 | 1.9375 |
| recDevs_pt.49 | 0.0835 | 0.0766 | -0.00017 | 0.9171 |
| recDevs_pt.50 | -0.0337 | 0.0889 | -0.005 | 2.6366 |
| recDevs_pt.51 | -0.1558 | 0.0904 | -0.001 | 0.5805 |
| recDevs_pt.52 | -0.2887 | 0.0994 | -0.00092 | 0.3442 |
| recDevs_pt.53 | -0.2284 | 0.0875 | -0.0036 | 0.3832 |
| recDevs_pt.54 | -0.2845 | 0.0900 | -0.003 | 0.3163 |
| recDevs_pt.55 | -0.1711 | 0.0767 | 0.0041 | 0.4484 |
| recDevs_pt.56 | -0.1778 | 0.0824 | -0.00075 | 0.4635 |
| recDevs_pt.57 | -0.0125 | 0.0693 | -0.0035 | 5.5236 |
| recDevs_pt.58 | -0.1347 | 0.0841 | -0.00024 | 0.6245 |
| recDevs_pt.59 | -0.1562 | 0.0825 | -0.00064 | 0.5281 |
| recDevs_pt.60 | -0.0043 | 0.0730 | -0.00069 | 17.1329 |
| recDevs_pt.61 | 0.0528 | 0.0691 | -0.0019 | 1.3094 |
| recDevs_pt.62 | 0.0182 | 0.0736 | 0.0025 | 4.0419 |
| recDevs_pt.63 | -0.1644 | 0.0932 | 0.0014 | 0.567 |
| recDevs_pt.64 | -0.0931 | 0.0865 | 0.0019 | 0.9292 |
| omegaM_pt | 0.0169 | 0.8480 | 0.0071 | 50.3158 |
| omegaM_pt.1 | 0.0480 | 0.8848 | 0.0072 | 18.4353 |
| omegaM_pt.2 | 0.0655 | 0.9031 | 0.0072 | 13.7822 |
| omegaM_pt.3 | 0.0098 | 0.9031 | 0.0071 | 91.7251 |
| omegaM_pt.4 | -0.0137 | 0.9081 | 0.0068 | 66.2605 |
| omegaM_pt.5 | 0.0439 | 0.9148 | 0.0066 | 20.8415 |
| omegaM_pt.6 | 0.1330 | 0.9318 | 0.0063 | 7.0061 |
| omegaM_pt.7 | 0.2417 | 0.9243 | 0.006 | 3.8245 |
| omegaM_pt.8 | 0.4292 | 0.9008 | 0.0057 | 2.099 |
| omegaM_pt.9 | 0.4717 | 0.9000 | 0.0057 | 1.9081 |
| omegaM_pt.10 | 0.4061 | 0.8991 | 0.0057 | 2.2142 |
| omegaM_pt.11 | 0.4288 | 0.8671 | 0.0057 | 2.0224 |
| omegaM_pt.12 | 0.3615 | 0.8293 | 0.0059 | 2.2942 |
| omegaM_pt.13 | 0.2493 | 0.8333 | 0.0061 | 3.3427 |
| omegaM_pt.14 | 0.0552 | 0.9094 | 0.0064 | 16.473 |
| omegaM_pt.15 | -0.1361 | 0.8875 | 0.0066 | 6.52 |
| omegaM_pt.16 | -0.2713 | 0.8377 | 0.0065 | 3.0875 |
| omegaM_pt.17 | -0.4137 | 0.8920 | 0.0064 | 2.1561 |
| omegaM_pt.18 | -0.5054 | 0.9198 | 0.0064 | 1.8198 |
| omegaM_pt.19 | -0.5333 | 0.9325 | 0.0065 | 1.7485 |
| omegaM_pt.20 | -0.5567 | 0.9354 | 0.0067 | 1.6802 |
| omegaM_pt.21 | -0.5105 | 0.9299 | 0.0068 | 1.8216 |
| omegaM_pt.22 | -0.2829 | 0.9212 | 0.0069 | 3.2567 |
| omegaM_pt.23 | 0.0831 | 0.9158 | 0.0068 | 11.0253 |
| omegaM_pt.24 | 0.4098 | 0.9145 | 0.0067 | 2.2317 |
| omegaM_pt.25 | 0.6511 | 0.9175 | 0.0065 | 1.4092 |
| omegaM_pt.26 | 0.6719 | 0.9201 | 0.0064 | 1.3694 |
| omegaM_pt.27 | 0.6924 | 0.9188 | 0.0065 | 1.327 |
| omegaM_pt.28 | 0.6800 | 0.9248 | 0.0063 | 1.36 |
| omegaM_pt.29 | 0.5284 | 0.9347 | 0.0062 | 1.7692 |
| omegaM_pt.30 | 0.2550 | 0.9356 | 0.0061 | 3.6691 |
| omegaM_pt.31 | -0.0622 | 0.9316 | 0.0061 | 14.9751 |
| omegaM_pt.32 | -0.3183 | 0.9283 | 0.0063 | 2.9167 |
| omegaM_pt.33 | -0.4786 | 0.9298 | 0.0066 | 1.9429 |
| omegaM_pt.34 | -0.6408 | 0.9294 | 0.0067 | 1.4504 |
| omegaM_pt.35 | -0.4821 | 0.9251 | 0.0069 | 1.9189 |
| omegaM_pt.36 | -0.3030 | 0.9214 | 0.0069 | 3.0407 |
| omegaM_pt.37 | -0.1468 | 0.9219 | 0.0069 | 6.281 |
| omegaM_pt.38 | 0.0009 | 0.9211 | 0.0068 | 1035.5102 |
| omegaM_pt.39 | 0.1283 | 0.9231 | 0.0067 | 7.1959 |
| omegaM_pt.40 | 0.1584 | 0.9262 | 0.0066 | 5.8472 |
| omegaM_pt.41 | 0.1458 | 0.9308 | 0.0063 | 6.3856 |
| omegaM_pt.42 | 0.0927 | 0.9303 | 0.006 | 10.036 |
| omegaM_pt.43 | 0.0483 | 0.9281 | 0.0056 | 19.2034 |
| omegaM_pt.44 | 0.1313 | 0.9282 | 0.005 | 7.0672 |
| omegaM_pt.45 | 0.2386 | 0.9256 | 0.0042 | 3.8789 |
| omegaM_pt.46 | 0.2834 | 0.9208 | 0.0033 | 3.2496 |
| omegaM_pt.47 | 0.2309 | 0.9241 | 0.0026 | 4.0023 |
| omegaM_pt.48 | -0.0007 | 0.9337 | 0.002 | 1359.7599 |
| omegaM_pt.49 | -0.2199 | 0.9403 | 0.0015 | 4.2766 |
| omegaM_pt.50 | -0.2656 | 0.9425 | 0.0012 | 3.5492 |
| omegaM_pt.51 | -0.2240 | 0.9421 | 0.00094 | 4.206 |
| omegaM_pt.52 | -0.2627 | 0.9447 | 7e-04 | 3.5957 |
| omegaM_pt.53 | -0.4825 | 0.9482 | 5e-04 | 1.9653 |
| omegaM_pt.54 | -0.7410 | 0.9504 | 0.00029 | 1.2826 |
| omegaM_pt.55 | -0.9050 | 0.9515 | 6e-05 | 1.0514 |
| omegaM_pt.56 | -0.8465 | 0.9508 | 4.1e-06 | 1.1233 |
| omegaM_pt.57 | -0.6492 | 0.9517 | -1.5e-05 | 1.466 |
| omegaM_pt.58 | -0.4425 | 0.9541 | -4.8e-05 | 2.156 |
| omegaM_pt.59 | -0.3202 | 0.9562 | -9.5e-05 | 2.9865 |
| omegaM_pt.60 | -0.1885 | 0.9587 | -0.00015 | 5.0862 |
| omegaM_pt.61 | -0.1018 | 0.9610 | -0.00019 | 9.4448 |
| omegaM_pt.62 | -0.0165 | 0.9636 | -2e-04 | 58.3323 |
| omegaM_pt.63 | 0.0512 | 0.9676 | -0.00018 | 18.8953 |
| omegaM_pt.64 | 0.1117 | 0.9714 | -2e-04 | 8.6967 |
| omegaM_pt.65 | 0.1796 | 0.9752 | -0.00022 | 5.4282 |
| omegaM_pt.66 | 0.1378 | 0.9927 | -0.00016 | 7.203 |
| omegaM_pt.67 | 0.0578 | 1.0009 | -7.5e-05 | 17.3215 |
| lnqComb_pg | -0.9712 | 0.1112 | -0.00063 | 0.1145 |
| lnqComb_pg.1 | -0.0036 | 0.0100 | -0.002 | 2.7783 |
| logitphi1_g | 0.4076 | 0.3937 | 0.00016 | 0.9659 |
| logitphi1_g.1 | 0.2732 | 0.2106 | -0.00035 | 0.771 |
| logitphi1_g.2 | 1.7081 | 0.3864 | -0.0076 | 0.2262 |
## Not Yet Implemented
Figure 24: Estimated correlation matrices for age composition residuals in the reduction fleet. The circles above the visualise the numbers below the diagonal.
Figure 25: Estimated correlation matrices for age composition residuals in the seineRoe fleet. The circles above the visualise the numbers below the diagonal.
Figure 26: Estimated correlation matrices for age composition residuals in the gillnet fleet. The circles above the visualise the numbers below the diagonal.
Figure 27: Plots of average age composition fits at the major stock level. Left is SISCA, right is ISCAM.
Figure 28: Comparison of spawning stock biomass and age-2 recruitment at the major stock level between ISCAM and SISCA.